The long hesitation is designed to make the original bettor think that the raise is a tough decision.
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In limit poker, when a player does nothing to discourage a sizable bet, then hesitates for a long time and chooses to make a large raise, there's little chance that he's bluffing. His long delay is an effort to make you think his raise is marginal and therefore weak. A player is more likely to have a winning hand if he takes longer than an average amount of time to act.
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Be careful and only pursue the pot with a medium to strong hand. If a raise is truly marginal, players are generally hesitant to let you know it, so they won't hesitate as long when deciding. Here's an opportunity to earn a profit by throwing away some pretty good hands. Remember, what you save by not calling is real money and it can buy real things.